Skip to content

Minor formatting proposals #1

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Minor formatting proposals #1

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
13 changes: 6 additions & 7 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,20 +1,20 @@
MethICA
========
# MethICA

Methylation signature analysis with independent component analysis.

Description: apply independent component analysis (ICA) to methylation data to extract epigenetic signatures and perform downstream analyses and representations to interpret the biological meaning of methylation components.

## Installation
========
Install from the GitHub repository using devtools:

Install from the GitHub repository using devtools:
```
install.packages("devtools")
library(devtools)
devtools::install_github("FunGeST/MethICA")
```

## Input files
========

For the extraction of methylation signature _MethICA_ requires one mandatory input file -- a **methylation level** file (bval) describing methylation levels of individual CpG sites or genomic regions (row) in each sample (column). Two additional files are needed for the interpretation of methylation components: a **CpG annotation** file describing the epigenetic context of CpG sites, and a **sample annotation** providing any relevant information about the samples.

**The input files should have the following format. Example input files are provided with the package.**
Expand Down Expand Up @@ -46,14 +46,13 @@ For the extraction of methylation signature _MethICA_ requires one mandatory inp
* `Sample`: Sample identifier. Any alphanumeric string.

## Running MethICA
================

* The [RUNNING\_METHICA\_EXAMPLE](https://github.com/FunGeST/MethICA) folder contains an example dataset and an R script of a typical MethICA analysis. Please try!</br>
* [*Introduction to MethICA*] provides a comprehensive example of the MethICA workflow with detailed explanations of each function.</br>


## License
========


Copyright (C) 2020 Léa Meunier

Expand Down